Wed Dec 21 14:21:37 PST 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Dec 21 2011 at 14:21:38 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6346490 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -4.318000 36.13700 ymin,ymax (A): -3.676000 49.52500 zmin,zma (A): -24.91100 31.18300 x,y,z range (A): 40.45500 53.20100 56.09400 scale (grids/A): 0.6346490 object centre (A): 15.90950 22.92450 3.136001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 90.24173 92.85661 90.35924 assigned negative charge : -285.8263 centred at (gu) : 90.35691 93.00046 90.27407 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5714 nv = 96 ne = 84 npr = 38331 no. pairs analyzed = 38331 no. exposed pairs = 2637 no. arc points = 18003 no. surface atoms = 897 nbur = 1067 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 380 mr = 3174 m= 2 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1866 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 6508 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2102976E-09 9.7470254E-09 midg,1,midg; midg,igrid,midg 7.1760389E-09 -1.5150068E-08 1,midg,midg; igrid,midg,midg 1.0600205E-08 -6.0573040E-09 gauss-seidel spectral radius is 0.9870901 estimated iterations to convergence 72 setup time was (sec) 0.7200000 now iterating at: 14:21:40 rms-change max change #iterations 0.1167860 19.53201 at 10iterations 1.1387504E-02 1.990200 at 20iterations 1.0801874E-03 0.1748750 at 30iterations 1.0725889E-04 1.7606735E-02 at 40iterations 1.0312298E-05 1.6717911E-03 at 50iterations finished qdiffx linear iterations at : 14:21:47 total time elapsed so far: 7.710000 # loops : 50 mean,max change (kT/e) : 1.0312298E-05 1.6717911E-03 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 14:21:51 7.879u 0.691s 0:12.59 67.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Dec 21 2011 at 14:21:51 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.903947 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -4.318000 36.13700 ymin,ymax (A): -3.676000 49.52500 zmin,zma (A): -24.91100 31.18300 x,y,z range (A): 40.45500 53.20100 56.09400 scale (grids/A): 1.903947 object centre (A): 15.90950 22.92450 3.136001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 90.72508 98.56992 91.07762 assigned negative charge : -285.8263 centred at (gu) : 91.07092 99.00146 90.82240 start vw surface at 0.1000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 60391 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18003 grid for indexing accessible points = 1.400000 m= 25158 mr = 41474 m= 4648 mr = 19653 m= 259 mr = 3256 m= 2 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 167 time to turn everything in is 0.6300000 number of dielectric boundary points 25967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 14434 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6346490 object centre at (A) : 15.90950 22.92450 3.136001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1978473E-02 1.7806830E-02 midg,1,midg; midg,igrid,midg 3.0758036E-02 -1.6001910E-02 1,midg,midg; igrid,midg,midg 3.1525460E-03 -4.9768109E-03 gauss-seidel spectral radius is 0.9985649 estimated iterations to convergence 209 setup time was (sec) 1.180000 now iterating at: 14:21:53 rms-change max change #iterations 3.531921 201.4072 at 10iterations 1.616596 69.94630 at 20iterations 0.7483615 26.10941 at 30iterations 0.3417230 11.39005 at 40iterations 0.1570361 5.448437 at 50iterations 7.2032668E-02 3.063148 at 60iterations 3.3122793E-02 1.349514 at 70iterations 1.5218789E-02 0.5368710 at 80iterations 6.9895061E-03 0.2295895 at 90iterations 3.2012581E-03 0.1219580 at 100iterations 1.4683179E-03 5.0423145E-02 at 110iterations 6.7682192E-04 2.6369095E-02 at 120iterations finished qdiffx linear iterations at : 14:22:07 total time elapsed so far: 14.90000 # loops : 120 mean,max change (kT/e) : 6.7682192E-04 2.6369095E-02 energy calculations done at 14.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.07000 DelPhi exited at 14:22:13 15.072u 0.968s 0:22.24 72.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Dec 21 2011 at 14:22:15 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.855920 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -4.318000 36.13700 ymin,ymax (A): -3.676000 49.52500 zmin,zma (A): -24.91100 31.18300 x,y,z range (A): 40.45500 53.20100 56.09400 scale (grids/A): 2.855920 object centre (A): 15.90950 22.92450 3.136001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 91.08775 102.8550 91.61652 assigned negative charge : -285.8263 centred at (gu) : 91.60643 103.5022 91.23370 start vw surface at 0.1000000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 138941 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18003 grid for indexing accessible points = 1.400000 m= 76910 mr = 99761 m= 32704 mr = 64441 m= 8832 mr = 27702 m= 1244 mr = 7193 m= 75 mr = 877 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 678 time to turn everything in is 1.350000 number of dielectric boundary points 58692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 14656 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.903947 object centre at (A) : 15.90950 22.92450 3.136001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8653073 4.5716297E-02 midg,1,midg; midg,igrid,midg 0.3234624 -0.2184050 1,midg,midg; igrid,midg,midg 1.5191575E-02 -2.8378345E-02 gauss-seidel spectral radius is 0.9992287 estimated iterations to convergence 284 setup time was (sec) 1.790000 now iterating at: 14:22:17 rms-change max change #iterations 8.428936 579.7250 at 10iterations 4.860482 137.9938 at 20iterations 2.775055 62.78918 at 30iterations 1.585886 33.55277 at 40iterations 0.9045980 19.20016 at 50iterations 0.5140168 12.60796 at 60iterations 0.2936108 6.329973 at 70iterations 0.1661667 3.331761 at 80iterations 9.4327495E-02 1.855217 at 90iterations 5.3633127E-02 1.120701 at 100iterations 3.0414870E-02 0.6872777 at 110iterations 1.7262466E-02 0.3261390 at 120iterations 9.7962664E-03 0.2210917 at 130iterations 5.5626435E-03 0.1056910 at 140iterations 3.1526734E-03 6.8695068E-02 at 150iterations 1.7895169E-03 3.8280487E-02 at 160iterations 1.0188988E-03 1.9484520E-02 at 170iterations 5.8063545E-04 1.2161255E-02 at 180iterations finished qdiffx linear iterations at : 14:22:39 total time elapsed so far: 23.75000 # loops : 180 mean,max change (kT/e) : 5.8063545E-04 1.2161255E-02 energy calculations done at 23.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.95000 DelPhi exited at 14:22:43 23.954u 0.576s 0:28.07 87.3% 0+0k 0+0io 0pf+0w